agat

AGAT (Atomic Graph ATtention networks)

Using AGAT

The documentation of AGAT API is available.

Installation

Install with conda environment

• Download the agat_linux_gpu_cu124.yml file.

• Run

  conda env create -f agat_linux_gpu_cu124.yml
  

• Install CUDA and CUDNN [Optional].

  • For HPC, you may load CUDA by checking module av, or you can contact your administrator for help.
  • CUDA Toolkit
  • cuDNN

• More installation options: Customized installation

Quick start

Prepare VASP calculations

Run VASP calculations at this step.

Collect paths of VASP calculations

• We provided examples of VASP outputs at VASP_calculations_example.

• Find all directories containing OUTCAR file:

  find . -name OUTCAR > paths.log
  

• Remove the string 'OUTCAR' in paths.log.

  sed -i 's/OUTCAR$//g' paths.log
  

• Specify the absolute paths in paths.log.

  sed -i "s#^.#${PWD}#g" paths.log
  

Build database

from agat.data import BuildDatabase
if __name__ == '__main__':
    database = BuildDatabase(mode_of_NN='ase_dist', num_of_cores=16)
    dataset = database.build()

Train AGAT model

from agat.model import Fit
f = Fit()
f.fit()

Application (geometry optimization)

from ase.optimize import BFGS
from ase.io import read
from agat.app import AgatCalculator

model_save_dir = 'agat_model'
graph_build_scheme_dir = 'dataset'

atoms = read('POSCAR')
calculator=AgatCalculator(model_save_dir,
                          graph_build_scheme_dir)
atoms = Atoms(atoms, calculator=calculator)
dyn = BFGS(atoms, trajectory='test.traj')
dyn.run(fmax=0.05)

Application (high-throughput prediction)

from agat.app.cata import HtAds

model_save_dir = 'agat_model'
graph_build_scheme_dir = 'dataset'
formula='NiCoFePdPt'

ha = HtAds(model_save_dir=model_save_dir, graph_build_scheme_dir=graph_build_scheme_dir)
ha.run(formula=formula)

Tips:

See API doc for more details. For example:

• Manipulating agat.dataset:
• AGAT molecular dynamics simulations:
• More options for controlling the AGAT training process: docs/sphinx/source/Default parameters.md.

Some default parameters

agat/default_parameters.py; Explanations: docs/sphinx/source/Default parameters.md.

Package structure

Change log

Please check Change_log.md